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freebayes: add v1.3.5, move to MesonPackage (#23772)

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Desmond Orton 2021-05-28 09:07:52 -06:00 committed by GitHub
parent a9197d6e6d
commit e0fa0145e3
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1 changed files with 28 additions and 2 deletions
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30
var/spack/repos/builtin/packages/freebayes/package.py
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@ -6,27 +6,53 @@
from spack import * from spack import *
class Freebayes(MakefilePackage): class Freebayes(MesonPackage):
"""Bayesian haplotype-based genetic polymorphism discovery and """Bayesian haplotype-based genetic polymorphism discovery and
genotyping.""" genotyping."""
homepage = "https://github.com/ekg/freebayes" homepage = "https://github.com/ekg/freebayes"
url = "https://github.com/freebayes/freebayes/releases/download/v1.3.5/freebayes-1.3.5-src.tar.gz"
git = "https://github.com/ekg/freebayes.git" git = "https://github.com/ekg/freebayes.git"
version('1.3.5', sha256='7e2635690e916ed85cec36b3263e6e5357413a4f2bf3035362d9749335e8a696')
version('1.1.0', commit='39e5e4bcb801556141f2da36aba1df5c5c60701f', version('1.1.0', commit='39e5e4bcb801556141f2da36aba1df5c5c60701f',
submodules=True) submodules=True, deprecated=True)
depends_on('cmake', type='build') depends_on('cmake', type='build')
depends_on('zlib') depends_on('zlib')
# Deps for @1.3.5 and beyond
depends_on('ninja', type='build', when='@1.3.5:')
depends_on('htslib', when='@1.3.5:')
depends_on('zlib', when='@1.3.5:')
depends_on('xz', when='@1.3.5:')
depends_on('parallel', when='@1.3.5:')
depends_on('vcftools', when='@1.3.5:')
depends_on('bc', when='@1.3.5:')
depends_on('samtools', when='@1.3.5:')
parallel = False parallel = False
@when('@:1.1.0')
def edit(self, spec, prefix): def edit(self, spec, prefix):
makefile = FileFilter('Makefile') makefile = FileFilter('Makefile')
b = prefix.bin b = prefix.bin
makefile.filter('cp bin/freebayes bin/bamleftalign /usr/local/bin/', makefile.filter('cp bin/freebayes bin/bamleftalign /usr/local/bin/',
'cp bin/freebayes bin/bamleftalign {0}'.format(b)) 'cp bin/freebayes bin/bamleftalign {0}'.format(b))
@when('@:1.1.0')
@run_before('install') @run_before('install')
def make_prefix_dot_bin(self): def make_prefix_dot_bin(self):
mkdir(prefix.bin) mkdir(prefix.bin)
@when('@:1.1.0')
def meson(self, spec, prefix):
pass
@when('@:1.1.0')
def build(self, spec, prefix):
make()
@when('@:1.1.0')
def install(self, spec, prefix):
make('install')